When I test the latest Trellis with all the defaults except adding your repo: git@github.com:rukawaxz/shenmueis2.git everything works successfully. (ansible 1.9.4)
On occasions that people have a number of failed iterations during their first Trellis project, it seems possible to arrive at the correct setup and configs but have the provisioning still not succeed because the server has become so tangled up during all the trial and error. You might find that, like has been common for others with many failed iterations, you can just wipe the server and successfully run server.yml and deploy with your latest configs.
If that still doesn’t work, could you check one more thing? You replied that the releases directory doesn’t seem to have the files from your rukawaxz/shenmueis2 project, but could you also check /srv/www/shenmueis.com/shared/source on the remote server for whether it has your project files (like composer.json)? If the files are there, then your repo is being cloned correctly but somehow the git archive command isn’t copying them over to the releases directory.
In any case, if trying again with a fresh server doesn’t work, then with all that you’ve learned…
I think if you make a fresh clone of the latest Trellis you’ll understand enough now to work through the setup steps in the README and have a successful provision and deploy.
One supporting argument for cloning the latest Trellis and working from its README and the Trellis docs are that they will be up to date. I skimmed over the setup tutorial you linked to and it looked pretty good but I noticed at least one item that was out-of-date related to ssh keys (github_ssh_keys was replaced with users 6 months ago; more info in ssh-keys docs).